Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 16 of 129
Found at i:2909353 original size:9 final size:9
Alignment explanation
Indices: 2909339--2909363 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2909329 TGACATGTGT
2909339 TTTATTTTA
1 TTTATTTTA
2909348 TTTATTTTA
1 TTTATTTTA
2909357 TTTATTT
1 TTTATTT
2909364 GTTAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTTA
Found at i:2910518 original size:18 final size:18
Alignment explanation
Indices: 2910483--2910524 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2910473 TGTTAATTTT
*
2910483 AAAATAAACTTTAAAATA
1 AAAATAAACTTCAAAATA
*
2910501 AAAATAAACTTCATAATA
1 AAAATAAACTTCAAAATA
*
2910519 ATAATA
1 AAAATA
2910525 TAAATTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATAAACTTCAAAATA
Found at i:2915216 original size:2 final size:2
Alignment explanation
Indices: 2915209--2915244 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2915199 AAGGCCAAAA
2915209 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2915245 ATAATTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2916170 original size:15 final size:15
Alignment explanation
Indices: 2916140--2916168 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2916130 AAATTTACGA
2916140 ATCTATTAAATTTTT
1 ATCTATTAAATTTTT
2916155 ATCTA-TAAATTTTT
1 ATCTATTAAATTTTT
2916169 TAAATTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (15 bp):
ATCTATTAAATTTTT
Found at i:2928439 original size:12 final size:12
Alignment explanation
Indices: 2928395--2928440 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
2928385 AAATTTATAT
*
2928395 ATTTATATTATA
1 ATTTATATAATA
2928407 ATTTATATAA-A
1 ATTTATATAATA
*
2928418 ATTATGTATAATA
1 ATT-TATATAATA
2928431 ATTTATATAA
1 ATTTATATAA
2928441 ATATAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 4 0.14
12 21 0.72
13 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (12 bp):
ATTTATATAATA
Found at i:2928451 original size:7 final size:7
Alignment explanation
Indices: 2928434--2928465 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2928424 TATAATAATT
2928434 TATATAAA
1 TATA-AAA
2928442 TATAAAA
1 TATAAAA
2928449 TATAAAA
1 TATAAAA
2928456 TATAAAA
1 TATAAAA
2928463 TAT
1 TAT
2928466 TTTTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (7 bp):
TATAAAA
Found at i:2928519 original size:24 final size:23
Alignment explanation
Indices: 2928470--2928521 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2928460 AAATATTTTT
*
2928470 TATT-TTATTAAAATTATATATA
1 TATTATTATTAAAATTATAAATA
*
2928492 -ATTATTATTAAAATTTTAAATTA
1 TATTATTATTAAAATTATAAA-TA
2928515 TATTATT
1 TATTATT
2928522 TTTATATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 3 0.12
22 14 0.56
23 2 0.08
24 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTATTATTAAAATTATAAATA
Found at i:2928528 original size:11 final size:11
Alignment explanation
Indices: 2928512--2928572 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
2928502 AAATTTTAAA
2928512 TTATATTATTT
1 TTATATTATTT
* *
2928523 TTATATCTAGTA
1 TTATAT-TATTT
2928535 TT-T-TTATTT
1 TTATATTATTT
*
2928544 TTATTTTTATTT
1 TTA-TATTATTT
*
2928556 TTATATTATAT
1 TTATATTATTT
2928567 TTATAT
1 TTATAT
2928573 CATATTATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 5 0.12
10 1 0.03
11 20 0.50
12 14 0.35
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (11 bp):
TTATATTATTT
Found at i:2928542 original size:6 final size:6
Alignment explanation
Indices: 2928533--2928559 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2928523 TTATATCTAG
2928533 TATTTT TATTTT TATTTT TATTTT TAT
1 TATTTT TATTTT TATTTT TATTTT TAT
2928560 ATTATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:2928581 original size:33 final size:33
Alignment explanation
Indices: 2928517--2928581 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
2928507 TTAAATTATA
* *
2928517 TTATTTTTATATCTAGTATTTTTATTTTTATTT
1 TTATTTTTATATCTAGTATTTATATTATTATTT
2928550 TTATTTTTATAT-TA-TATTTATATCATATTATT
1 TTATTTTTATATCTAGTATTTATAT--TATTATT
2928582 ACCTCATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 8 0.29
32 2 0.07
33 18 0.64
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (33 bp):
TTATTTTTATATCTAGTATTTATATTATTATTT
Found at i:2931134 original size:14 final size:14
Alignment explanation
Indices: 2931115--2931168 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
2931105 ATACGATATG
2931115 ATAATATAATATAA
1 ATAATATAATATAA
2931129 AT-A-ATAA-ATAA
1 ATAATATAATATAA
*
2931140 ATAATA-ATATAAAA
1 ATAATATA-ATATAA
*
2931154 ATAATATAATTTAA
1 ATAATATAATATAA
2931168 A
1 A
2931169 ATTTTAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
11 6 0.19
12 6 0.19
13 3 0.09
14 16 0.50
15 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATATAATATAA
Found at i:2931139 original size:11 final size:12
Alignment explanation
Indices: 2931120--2931162 Score: 72
Period size: 11 Copynumber: 3.8 Consensus size: 12
2931110 ATATGATAAT
2931120 ATAATATAAATA
1 ATAATATAAATA
2931132 ATAA-ATAAATA
1 ATAATATAAATA
2931143 ATAATATAAA-A
1 ATAATATAAATA
2931154 ATAATATAA
1 ATAATATAA
2931163 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:2932583 original size:20 final size:20
Alignment explanation
Indices: 2932554--2932591 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2932544 TTTTGTATTA
2932554 AAAATGAATAAATTAAAATT
1 AAAATGAATAAATTAAAATT
* *
2932574 AAAATTAATATATTAAAA
1 AAAATGAATAAATTAAAA
2932592 GATTTTGTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAATGAATAAATTAAAATT
Found at i:2939443 original size:20 final size:19
Alignment explanation
Indices: 2939396--2939443 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
2939386 GATGGACGGA
2939396 GAAAGAGGAAAAGAAAGGG
1 GAAAGAGGAAAAGAAAGGG
* * *
2939415 GAAGCGAGGAAGAGAGAGAGG
1 GAA-AGAGGAAAAGAAAG-GG
2939436 GAAAGAGG
1 GAAAGAGG
2939444 GAACGAAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.13
20 15 0.65
21 5 0.22
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (19 bp):
GAAAGAGGAAAAGAAAGGG
Found at i:2939705 original size:13 final size:13
Alignment explanation
Indices: 2939687--2939714 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2939677 CAGAAACGAC
2939687 AGTTTACAGTTAA
1 AGTTTACAGTTAA
2939700 AGTTTACAGTTAA
1 AGTTTACAGTTAA
2939713 AG
1 AG
2939715 GGAATGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (13 bp):
AGTTTACAGTTAA
Found at i:2955800 original size:28 final size:29
Alignment explanation
Indices: 2955769--2955832 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 29
2955759 TATTAAAATA
2955769 ATTTTAAA-TATATAATATATAAT-TA-TTT
1 ATTTTAAATTAT-TAA-ATATAATATATTTT
*
2955797 ATTTTAAATTATTAAATGTAATATATTTT
1 ATTTTAAATTATTAAATATAATATATTTT
2955826 ATTTTAA
1 ATTTTAA
2955833 TTTAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 6 0.19
28 13 0.41
29 13 0.41
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
ATTTTAAATTATTAAATATAATATATTTT
Found at i:2955845 original size:34 final size:34
Alignment explanation
Indices: 2955781--2955846 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
2955771 TTTAAATATA
* **
2955781 TAATATATAATTATTTATTTTAAATTATTAAATG
1 TAATATATAATTATTTAATTTAAAAAATTAAATG
*
2955815 TAATATAT-TTTATTTTAATTTAAAAAATTAAA
1 TAATATATAATTA-TTTAATTTAAAAAATTAAA
2955847 AAATTTATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 3 0.11
34 24 0.89
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (34 bp):
TAATATATAATTATTTAATTTAAAAAATTAAATG
Found at i:2955988 original size:14 final size:14
Alignment explanation
Indices: 2955968--2956006 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2955958 TAAATATTAA
2955968 TTTTAATA-AAATT
1 TTTTAATATAAATT
2955981 TATTTAATATAAATT
1 T-TTTAATATAAATT
*
2955996 TTTTATTATAA
1 TTTTAATATAA
2956007 TTATAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 16 0.70
15 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAATATAAATT
Found at i:2956002 original size:18 final size:21
Alignment explanation
Indices: 2955965--2956022 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
2955955 ATTTAAATAT
* **
2955965 TAATTTTAATAAAATTTATT-
1 TAATTATAATAATTTTTATTA
*
2955985 TAA-TATAA-ATTTTTTATTA
1 TAATTATAATAATTTTTATTA
2956004 TAATTATAATAATTTTTAT
1 TAATTATAATAATTTTTAT
2956023 AATTATTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
18 7 0.23
19 7 0.23
20 8 0.27
21 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATTATAATAATTTTTATTA
Found at i:2956614 original size:5 final size:5
Alignment explanation
Indices: 2956594--2956641 Score: 78
Period size: 5 Copynumber: 9.4 Consensus size: 5
2956584 TTTTTAATTT
*
2956594 TTAAT TTAAA TATAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA TTAAA T-TAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TT
2956642 TTATTGATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
5 36 0.88
6 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:2958010 original size:12 final size:12
Alignment explanation
Indices: 2957995--2958044 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
2957985 AAATTTATTT
2957995 TTTAATTATATA
1 TTTAATTATATA
2958007 TTTAATT-T-TA
1 TTTAATTATATA
* *
2958017 TATATTTATATA
1 TTTAATTATATA
* *
2958029 TATAATTTTATA
1 TTTAATTATATA
2958041 TTTA
1 TTTA
2958045 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 7 0.23
11 2 0.06
12 22 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTAATTATATA
Found at i:2958025 original size:22 final size:22
Alignment explanation
Indices: 2958000--2958041 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2957990 TATTTTTTAA
*
2958000 TTATATATTTAATTTTATATAT
1 TTATATATATAATTTTATATAT
2958022 TTATATATATAATTTTATAT
1 TTATATATATAATTTTATAT
2958042 TTATATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATATATAATTTTATATAT
Found at i:2958032 original size:14 final size:14
Alignment explanation
Indices: 2958001--2958050 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
2957991 ATTTTTTAAT
*
2958001 TATATATTTA-ATTT
1 TATATATTTATA-TA
2958015 TATATATTTATATA
1 TATATATTTATATA
2958029 TATA-ATTT-TATA
1 TATATATTTATATA
*
2958041 TTTATATTTA
1 TATATATTTA
2958051 AAATAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 7 0.23
13 8 0.26
14 15 0.48
15 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATATATTTATATA
Found at i:2965521 original size:31 final size:32
Alignment explanation
Indices: 2965475--2965576 Score: 102
Period size: 31 Copynumber: 3.2 Consensus size: 32
2965465 GTGAAATAAA
* *
2965475 ATATTAAAATTTATATATTTTTATTATATTTT
1 ATATAAAAATATATATATTTTTATTATATTTT
* * *
2965507 ATATAAAAA-ATATATATTATAATT-TATATTA
1 ATATAAAAATATATATATTTTTATTATAT-TTT
*
2965538 ATATAAAAATATAAATATATTTTTATTA-AATTT
1 ATATAAAAATAT--ATATATTTTTATTATATTTT
2965571 ATATAA
1 ATATAA
2965577 TTATAACCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
30 3 0.05
31 23 0.41
32 10 0.18
33 8 0.14
34 12 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATATAAAAATATATATATTTTTATTATATTTT
Found at i:2965548 original size:30 final size:29
Alignment explanation
Indices: 2965498--2965566 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 29
2965488 TATATTTTTA
* *
2965498 TTATATTTTATATAAAAAATATATATTATAAT
1 TTATA-TTAATATAAAAAATATA-AATAT-AT
2965530 TTATATTAATAT-AAAAATATAAATATAT
1 TTATATTAATATAAAAAATATAAATATAT
*
2965558 TTTTATTAA
1 TTATATTAA
2965567 ATTTATATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.29
29 4 0.12
30 9 0.26
31 6 0.18
32 5 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TTATATTAATATAAAAAATATAAATATAT
Found at i:2966466 original size:22 final size:20
Alignment explanation
Indices: 2966441--2966481 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
2966431 TAAGAGTTCA
*
2966441 ATTAATTATAATTCAAATATTG
1 ATTAATT-TAAATC-AATATTG
2966463 ATTAATTTAAATCAATATT
1 ATTAATTTAAATCAATATT
2966482 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (20 bp):
ATTAATTTAAATCAATATTG
Found at i:2975599 original size:437 final size:437
Alignment explanation
Indices: 2974785--2975660 Score: 1734
Period size: 437 Copynumber: 2.0 Consensus size: 437
2974775 GTCCTGCATT
2974785 TTACTTCTTTAATACTTTGTTGCACCATACAAAAGTAAGGGATTGGAAGTACCTATATTCAGCAT
1 TTACTTCTTTAATACTTTGTTGCACCATACAAAAGTAAGGGATTGGAAGTACCTATATTCAGCAT
2974850 GCTTTCATCTTAGATTTACAAAATAGAACAGAATTAGATATTTTCTTGGAGCCATTTCTTGCCAA
66 GCTTTCATCTTAGATTTACAAAATAGAACAGAATTAGATATTTTCTTGGAGCCATTTCTTGCCAA
2974915 AGATTTTGGGAGTAGCTGAATCTGATCTGCATGTTGCCCCTTGCATCAAGATTTCATAGCAATGT
131 AGATTTTGGGAGTAGCTGAATCTGATCTGCATGTTGCCCCTTGCATCAAGATTTCATAGCAATGT
2974980 GCTTGTAATATAGGTTCTTATAATCATCAGGCAGACTTAATATAGAACTAGTGGGTTGAAATCAT
196 GCTTGTAATATAGGTTCTTATAATCATCAGGCAGACTTAATATAGAACTAGTGGGTTGAAATCAT
2975045 AGGTCTTTGTGGAGAATCACCTTTCACCCTATATTTGGTTTATTAAAAAGCATAACTGTTTTAGC
261 AGGTCTTTGTGGAGAATCACCTTTCACCCTATATTTGGTTTATTAAAAAGCATAACTGTTTTAGC
2975110 ATGGGGACGTGCTAATTGCTAGATTAAATTATCTAGAACTTTATTATGGGTTTGTGGAAAAACTA
326 ATGGGGACGTGCTAATTGCTAGATTAAATTATCTAGAACTTTATTATGGGTTTGTGGAAAAACTA
2975175 AGAAATAAATCAGTGTGAAAACTGAATGTATGTTGGAAAACTGCTTA
391 AGAAATAAATCAGTGTGAAAACTGAATGTATGTTGGAAAACTGCTTA
2975222 TTACTTCTTTAATACTTTGTTGCACCATACAAAAGTAAGGGATTGGAAGTACCTATATTCAGCAT
1 TTACTTCTTTAATACTTTGTTGCACCATACAAAAGTAAGGGATTGGAAGTACCTATATTCAGCAT
2975287 GCTTTCATCTTAGATTTACAAAATAGAACAGAATTAGATATTTTCTTGGAGCCATTTCTTGCCAA
66 GCTTTCATCTTAGATTTACAAAATAGAACAGAATTAGATATTTTCTTGGAGCCATTTCTTGCCAA
2975352 AGATTTTGGGAGTAGCTGAATCTGATCTGCATGTTGCCCCTTGCATCAAGATTTCATAGCAATGT
131 AGATTTTGGGAGTAGCTGAATCTGATCTGCATGTTGCCCCTTGCATCAAGATTTCATAGCAATGT
2975417 GCTTGTAATATAGGTTCTTATAATCATCAGGCAGACTTAATATAGAACTAGTGGGTTGAAATCAT
196 GCTTGTAATATAGGTTCTTATAATCATCAGGCAGACTTAATATAGAACTAGTGGGTTGAAATCAT
* *
2975482 AGGTCTTTGTGGGGAATCATCTTTCACCCTATATTTGGTTTATTAAAAAGCATAACTGTTTTAGC
261 AGGTCTTTGTGGAGAATCACCTTTCACCCTATATTTGGTTTATTAAAAAGCATAACTGTTTTAGC
2975547 ATGGGGACGTGCTAATTGCTAGATTAAATTATCTAGAACTTTATTATGGGTTTGTGGAAAAACTA
326 ATGGGGACGTGCTAATTGCTAGATTAAATTATCTAGAACTTTATTATGGGTTTGTGGAAAAACTA
2975612 AGAAATAAATCAGTGTGAAAACTGAATGTATGTTGGAAAACTGCTTA
391 AGAAATAAATCAGTGTGAAAACTGAATGTATGTTGGAAAACTGCTTA
2975659 TT
1 TT
2975661 GAGAATTATA
Statistics
Matches: 437, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
437 437 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (437 bp):
TTACTTCTTTAATACTTTGTTGCACCATACAAAAGTAAGGGATTGGAAGTACCTATATTCAGCAT
GCTTTCATCTTAGATTTACAAAATAGAACAGAATTAGATATTTTCTTGGAGCCATTTCTTGCCAA
AGATTTTGGGAGTAGCTGAATCTGATCTGCATGTTGCCCCTTGCATCAAGATTTCATAGCAATGT
GCTTGTAATATAGGTTCTTATAATCATCAGGCAGACTTAATATAGAACTAGTGGGTTGAAATCAT
AGGTCTTTGTGGAGAATCACCTTTCACCCTATATTTGGTTTATTAAAAAGCATAACTGTTTTAGC
ATGGGGACGTGCTAATTGCTAGATTAAATTATCTAGAACTTTATTATGGGTTTGTGGAAAAACTA
AGAAATAAATCAGTGTGAAAACTGAATGTATGTTGGAAAACTGCTTA
Found at i:2975791 original size:22 final size:22
Alignment explanation
Indices: 2975766--2975807 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2975756 TTGTCTATCC
* * *
2975766 TAATTTTAGGGATATAAATACT
1 TAATTCTAGAGATACAAATACT
2975788 TAATTCTAGAGATACAAATA
1 TAATTCTAGAGATACAAATA
2975808 TAAATATACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (22 bp):
TAATTCTAGAGATACAAATACT
Found at i:2979754 original size:22 final size:22
Alignment explanation
Indices: 2979729--2979770 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2979719 TTGTCTATCC
* *
2979729 TAATTTTAGGGATACAAATACT
1 TAATTCTAGAGATACAAATACT
2979751 TAATTCTAGAGATACAAATA
1 TAATTCTAGAGATACAAATA
2979771 TAAATATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
TAATTCTAGAGATACAAATACT
Found at i:2986368 original size:2 final size:2
Alignment explanation
Indices: 2986353--2986390 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2986343 AAAGTGTATG
* *
2986353 TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2986391 GTAATGATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2988418 original size:40 final size:40
Alignment explanation
Indices: 2988374--2988449 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
2988364 ATGATTATGT
2988374 ATAATTAATTGACAAATTACTTATCCCTAAATTACTCAAC
1 ATAATTAATTGACAAATTACTTATCCCTAAATTACTCAAC
* * * **
2988414 ATAATTAATTTATAATTTTTTTATCCCTAAATTACT
1 ATAATTAATTGACAAATTACTTATCCCTAAATTACT
2988450 TAATAAAGTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.01, T:0.43
Consensus pattern (40 bp):
ATAATTAATTGACAAATTACTTATCCCTAAATTACTCAAC
Found at i:2991320 original size:29 final size:29
Alignment explanation
Indices: 2991287--2991351 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
2991277 ATATTCTTCG
* *
2991287 ATTTTTAAGAATTTAGTCTTTATAATATT
1 ATTTTTAAAAATTTAGTCCTTATAATATT
* *
2991316 ATTTTAAAAAATTTTGTCCTTATAATATT
1 ATTTTTAAAAATTTAGTCCTTATAATATT
2991345 ATTTTTA
1 ATTTTTA
2991352 CCTATATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (29 bp):
ATTTTTAAAAATTTAGTCCTTATAATATT
Found at i:2991441 original size:29 final size:29
Alignment explanation
Indices: 2991409--2991471 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
2991399 TTGAATTGAA
2991409 TAAAATAATATTATAAGG-ATTAAATTTTT
1 TAAAATAATATTA-AAGGAATTAAATTTTT
* *
2991438 T-AAATAATATTAGAGGAATTAGATTTTT
1 TAAAATAATATTAAAGGAATTAAATTTTT
2991466 TAAAAT
1 TAAAAT
2991472 CGAAAAGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.10
28 22 0.73
29 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (29 bp):
TAAAATAATATTAAAGGAATTAAATTTTT
Found at i:2993949 original size:18 final size:19
Alignment explanation
Indices: 2993920--2993956 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2993910 TAAAATTCTT
2993920 TTTTTATATTTTAAAATTA
1 TTTTTATATTTTAAAATTA
*
2993939 TTTTTAT-TTTTAACATTA
1 TTTTTATATTTTAAAATTA
2993957 AAAATTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTATATTTTAAAATTA
Found at i:2994859 original size:2 final size:2
Alignment explanation
Indices: 2994852--2994881 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2994842 AATATGCATT
2994852 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2994882 AACCCAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2999383 original size:2 final size:2
Alignment explanation
Indices: 2999376--2999415 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2999366 CATTTTACCC
2999376 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2999416 ACATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2999423 original size:2 final size:2
Alignment explanation
Indices: 2999418--2999442 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2999408 CTCTCTCTAC
2999418 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2999443 ACAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3008088 original size:2 final size:2
Alignment explanation
Indices: 3008081--3008110 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3008071 TTTCCTCTGA
3008081 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3008111 TCTGAAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3010896 original size:17 final size:17
Alignment explanation
Indices: 3010874--3010918 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 17
3010864 AAATGTTAGT
3010874 ATGGAAATCAAACACCA
1 ATGGAAATCAAACACCA
3010891 ATGGAAGAAATCAAACACCA
1 AT-G--GAAATCAAACACCA
*
3010911 GTGGAAAT
1 ATGGAAAT
3010919 TTGAAGTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 7 0.29
18 1 0.04
19 1 0.04
20 15 0.62
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.13
Consensus pattern (17 bp):
ATGGAAATCAAACACCA
Found at i:3010902 original size:20 final size:20
Alignment explanation
Indices: 3010877--3010916 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3010867 TGTTAGTATG
3010877 GAAATCAAACACCAATGGAA
1 GAAATCAAACACCAATGGAA
*
3010897 GAAATCAAACACCAGTGGAA
1 GAAATCAAACACCAATGGAA
3010917 ATTTGAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.17, T:0.10
Consensus pattern (20 bp):
GAAATCAAACACCAATGGAA
Found at i:3012456 original size:23 final size:22
Alignment explanation
Indices: 3012430--3012477 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3012420 ATATATTATT
* *
3012430 TTTTGTTTATATTTAATTTTACA
1 TTTTATTTATATAT-ATTTTACA
*
3012453 TTTTATTTATATATATTTTATA
1 TTTTATTTATATATATTTTACA
3012475 TTT
1 TTT
3012478 AAAAATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTATTTATATATATTTTACA
Found at i:3013237 original size:23 final size:24
Alignment explanation
Indices: 3013205--3013260 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
3013195 ATATCGATAG
*
3013205 AATATAAATATAA-TATAAAATTAT
1 AATAAAAATATAAGT-TAAAATTAT
*
3013229 AA-AAAAATATAAGTTAAAATTTT
1 AATAAAAATATAAGTTAAAATTAT
3013252 AATAAAAAT
1 AATAAAAAT
3013261 GATATGAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
AATAAAAATATAAGTTAAAATTAT
Found at i:3024268 original size:27 final size:27
Alignment explanation
Indices: 3024236--3024288 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3024226 CCCTTTCCTT
3024236 TCTCTTTTAAAATTGATTGAT-GATTGC
1 TCTCTTTT-AAATTGATTGATGGATTGC
**
3024263 TCTCTTTTTGATTGATTGATGGATTG
1 TCTCTTTTAAATTGATTGATGGATTG
3024289 ATAGAATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (27 bp):
TCTCTTTTAAATTGATTGATGGATTGC
Found at i:3025017 original size:24 final size:23
Alignment explanation
Indices: 3024988--3025034 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
3024978 TCATTCACTC
*
3024988 ATTCATCATAACATGAATCATCAA
1 ATTCATCATAACA-CAATCATCAA
*
3025012 ATTCATCATAGCACAATCATCAA
1 ATTCATCATAACACAATCATCAA
3025035 CCAGCATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.45, C:0.23, G:0.04, T:0.28
Consensus pattern (23 bp):
ATTCATCATAACACAATCATCAA
Found at i:3025519 original size:23 final size:23
Alignment explanation
Indices: 3025467--3025532 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 23
3025457 TTTATACGTT
*
3025467 AATAAATCAAATGATAATATCTTATC
1 AATAAAT-AAAT-ATAA-ATCTTATA
3025493 AATAAATAAATATAAATCTT-TAA
1 AATAAATAAATATAAATCTTAT-A
* *
3025516 AATAAATATACATAAAT
1 AATAAATAAATATAAAT
3025533 TAAAATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 1 0.03
23 20 0.56
24 4 0.11
25 4 0.11
26 7 0.19
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAAATAAATATAAATCTTATA
Found at i:3028455 original size:26 final size:25
Alignment explanation
Indices: 3028403--3028456 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
3028393 AAATAGAAAT
3028403 AAAAATTATTATAATTATAATCGAAA
1 AAAAATTATTATAATTATAATC-AAA
* * *
3028429 AAAATTTATTATAATTATTATTAAA
1 AAAAATTATTATAATTATAATCAAA
3028454 AAA
1 AAA
3028457 TTTTAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (25 bp):
AAAAATTATTATAATTATAATCAAA
Found at i:3033039 original size:2 final size:2
Alignment explanation
Indices: 3033032--3033081 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3033022 TGAGGCCACC
3033032 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3033074 CT CT CT CT
1 CT CT CT CT
3033082 TATTCTCACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3039809 original size:2 final size:2
Alignment explanation
Indices: 3039802--3039836 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3039792 TCTCAAATAT
3039802 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3039837 ATCTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3042437 original size:22 final size:22
Alignment explanation
Indices: 3042409--3042450 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3042399 ATTTTTTAAA
*
3042409 AAAATTAATTTTTATTTATTTT
1 AAAATTAATATTTATTTATTTT
3042431 AAAATTAATATTTATTTATT
1 AAAATTAATATTTATTTATT
3042451 AATGAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AAAATTAATATTTATTTATTTT
Found at i:3045233 original size:2 final size:2
Alignment explanation
Indices: 3045226--3045250 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3045216 GAAAATAGTT
3045226 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3045251 TTAAGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3049914 original size:18 final size:20
Alignment explanation
Indices: 3049874--3049914 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3049864 TTAGCCTCAA
*
3049874 TTTTCTCTGTCTTTTTGTAT
1 TTTTCTCTGCCTTTTTGTAT
3049894 TTTTCTCT-CCTTTTTGT-T
1 TTTTCTCTGCCTTTTTGTAT
3049912 TTT
1 TTT
3049915 AATTTACGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.02, C:0.17, G:0.07, T:0.73
Consensus pattern (20 bp):
TTTTCTCTGCCTTTTTGTAT
Found at i:3050935 original size:18 final size:18
Alignment explanation
Indices: 3050885--3050935 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
3050875 TAAATTTAAA
*
3050885 ATTTTTAATAAAATTTGAT
1 ATTTTTAATAAAA-TAGAT
* *
3050904 A-TATTAATTAAATAGAT
1 ATTTTTAATAAAATAGAT
3050921 ATTTTTAATAAAATA
1 ATTTTTAATAAAATA
3050936 TTAATAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 5 0.19
18 20 0.77
19 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
ATTTTTAATAAAATAGAT
Found at i:3052232 original size:52 final size:52
Alignment explanation
Indices: 3052171--3052275 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
3052161 GTTAACATAG
*
3052171 TATTTAATATGATTGCAAAATCCTTAAGTCAATGATTTATACGTTATTGTTA
1 TATTTAATATGATTGCAAAATCCTTAAGTCAATGATTTATACGTTATTATTA
3052223 TATTTAATATGATTGCAAAATCCTTAAGTCAATGATTTATACGTTATTATTA
1 TATTTAATATGATTGCAAAATCCTTAAGTCAATGATTTATACGTTATTATTA
3052275 T
1 T
3052276 TATTATTCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (52 bp):
TATTTAATATGATTGCAAAATCCTTAAGTCAATGATTTATACGTTATTATTA
Found at i:3053000 original size:1 final size:1
Alignment explanation
Indices: 3052994--3053019 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3052984 CTATACTGTG
3052994 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3053020 GAAAGCTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3059759 original size:6 final size:6
Alignment explanation
Indices: 3059748--3059778 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3059738 CCTAGACCGG
3059748 GAAGCC GAAGCC GAAGCC GAAGCC GAAGCC G
1 GAAGCC GAAGCC GAAGCC GAAGCC GAAGCC G
3059779 TCGCCGCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.35, T:0.00
Consensus pattern (6 bp):
GAAGCC
Found at i:3065405 original size:14 final size:14
Alignment explanation
Indices: 3065386--3065415 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3065376 AATTTCATTC
*
3065386 ATAATTTTTTAATT
1 ATAATTTTATAATT
3065400 ATAATTTTATAATT
1 ATAATTTTATAATT
3065414 AT
1 AT
3065416 TTAATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATAATTTTATAATT
Found at i:3066432 original size:19 final size:18
Alignment explanation
Indices: 3066385--3066442 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
3066375 AGATCAACCA
3066385 TAAAA-TTATATGATTTTT
1 TAAAATTTATAT-ATTTTT
* *
3066403 TAATATATATACTATTTTT
1 TAAAATTTATA-TATTTTT
*
3066422 TAAAATTTATAATATTATT
1 TAAAATTTAT-ATATTTTT
3066441 TA
1 TA
3066443 TCAAAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 4 0.12
19 26 0.81
20 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TAAAATTTATATATTTTT
Found at i:3068800 original size:60 final size:60
Alignment explanation
Indices: 3068729--3068841 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 60
3068719 TATAAACATT
* * * *
3068729 TTACAATTTTAAGAATAACCAAAATTTTAATTCATATATTAAATAGGTAATATAAAATAA
1 TTACAAATTTAAGAAGAAACAAAATTTTAATTCACATATTAAATAGGTAATATAAAATAA
** * * *
3068789 TTACAAATTTAAGAAGAAACAAGTTTTTATTTCACGTATTAAATGGGTAATAT
1 TTACAAATTTAAGAAGAAACAAAATTTTAATTCACATATTAAATAGGTAATAT
3068842 TGATTATTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (60 bp):
TTACAAATTTAAGAAGAAACAAAATTTTAATTCACATATTAAATAGGTAATATAAAATAA
Found at i:3070340 original size:17 final size:19
Alignment explanation
Indices: 3070318--3070355 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
3070308 TCATTCTAGA
3070318 ATTTTTATATT-ATAT-TT
1 ATTTTTATATTCATATGTT
3070335 ATTTTTATATTCATATGTT
1 ATTTTTATATTCATATGTT
3070354 AT
1 AT
3070356 AAATATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 4 0.21
19 4 0.21
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (19 bp):
ATTTTTATATTCATATGTT
Found at i:3074476 original size:21 final size:22
Alignment explanation
Indices: 3074447--3074499 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
3074437 TTTTTTAATT
3074447 ATATATTTATA-TTTAAAAAATA
1 ATAT-TTTATATTTTAAAAAATA
3074469 ATATTTTATATTTTAAAAAATA
1 ATATTTTATATTTTAAAAAATA
3074491 ATATTTTAT
1 ATATTTTAT
3074500 TAATTTCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTTTATATTTTAAAAAATA
Found at i:3075094 original size:26 final size:24
Alignment explanation
Indices: 3075039--3075106 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 24
3075029 AAATATATAT
* *
3075039 AAATATATATTTTAA--AATTTAA
1 AAATATTTATTTTAATTAATCTAA
3075061 AAATATTTATTTTAATTAATCTAA
1 AAATATTTATTTTAATTAATCTAA
* *
3075085 ATAATAATTTATATTATTTAAT
1 A-AAT-ATTTATTTTAATTAAT
3075107 AAAAACTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.37
24 7 0.18
25 3 0.08
26 14 0.37
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (24 bp):
AAATATTTATTTTAATTAATCTAA
Found at i:3081332 original size:12 final size:12
Alignment explanation
Indices: 3081315--3081352 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
3081305 ATACATACAA
*
3081315 ATATATATATAT
1 ATATATGTATAT
3081327 ATATATGTATAT
1 ATATATGTATAT
*
3081339 ATGTATGTATAT
1 ATATATGTATAT
3081351 AT
1 AT
3081353 CTTCCACCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:3082491 original size:22 final size:21
Alignment explanation
Indices: 3082466--3082506 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
3082456 TTCTTTTCAA
3082466 TTTCT-CTGCTGTCTCGTGTTTC
1 TTTCTACTGCT-TCTC-TGTTTC
3082488 TTTCTACTGCTTCTCTGTT
1 TTTCTACTGCTTCTCTGTT
3082507 ATGTACGCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.02, C:0.27, G:0.15, T:0.56
Consensus pattern (21 bp):
TTTCTACTGCTTCTCTGTTTC
Found at i:3086955 original size:36 final size:36
Alignment explanation
Indices: 3086908--3086978 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
3086898 CAATTAATTC
*
3086908 ATATATATATATATATCTTGTTATATATTAAACAAG
1 ATATATATATATATATCTTGTTAGATATTAAACAAG
3086944 ATATATATATATATATCTTGTTAGATATTAAACAA
1 ATATATATATATATATCTTGTTAGATATTAAACAA
3086979 AAGAAAAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.44
Consensus pattern (36 bp):
ATATATATATATATATCTTGTTAGATATTAAACAAG
Found at i:3088464 original size:12 final size:12
Alignment explanation
Indices: 3088431--3088502 Score: 58
Period size: 12 Copynumber: 5.9 Consensus size: 12
3088421 ATTATATAAA
3088431 TAATTATTT-TT
1 TAATTATTTATT
*
3088442 TAATTAATTATT
1 TAATTATTTATT
*
3088454 TAATTTTTTATT
1 TAATTATTTATT
*
3088466 TATATATATTTATA
1 TA-AT-TATTTATT
*
3088480 TAATGATATT-TT
1 TAATTAT-TTATT
*
3088492 TAAATATTTAT
1 TAATTATTTAT
3088503 ATTTAAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
11 10 0.21
12 23 0.49
13 6 0.13
14 8 0.17
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (12 bp):
TAATTATTTATT
Found at i:3088493 original size:30 final size:30
Alignment explanation
Indices: 3088454--3088525 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 30
3088444 ATTAATTATT
* *
3088454 TAAT-TTTTTATTTATATATATTTATATAA
1 TAATATTTTTATTTATATATATTTAAAAAA
* ** *
3088483 TGATATTTTTAAATATTTATATTTAAAAAA
1 TAATATTTTTATTTATATATATTTAAAAAA
3088513 TAATA-TTTTATTT
1 TAATATTTTTATTT
3088526 TTTAAAAAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
TAATATTTTTATTTATATATATTTAAAAAA
Found at i:3088519 original size:20 final size:20
Alignment explanation
Indices: 3088494--3088546 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
3088484 GATATTTTTA
3088494 AATATTTATATTTAAAAAAT
1 AATATTTATATTTAAAAAAT
*
3088514 AATATTTTATTTTTTAAAAAAT
1 AATA-TTTA-TATTTAAAAAAT
3088536 AATATTT-TATT
1 AATATTTATATT
3088547 AATTTCAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 3 0.10
20 4 0.14
21 7 0.24
22 15 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTATATTTAAAAAAT
Found at i:3088532 original size:22 final size:22
Alignment explanation
Indices: 3088504--3088546 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3088494 AATATTTATA
3088504 TTTAAAAAATAATATTTTATTT
1 TTTAAAAAATAATATTTTATTT
3088526 TTTAAAAAATAATATTTTATT
1 TTTAAAAAATAATATTTTATT
3088547 AATTTCAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAAAAAATAATATTTTATTT
Found at i:3089847 original size:58 final size:58
Alignment explanation
Indices: 3089757--3089884 Score: 184
Period size: 58 Copynumber: 2.2 Consensus size: 58
3089747 TAACTGTGAT
* ** * * *
3089757 GACCGCAATAACTTTTGTTATGCCTGCAATCACGATAAACATAATGTGATCGAATTGC
1 GACCGCAATAGCTTCCGTTATGCCTGCAATCACGATAAACATAACGTGATCGAAATAC
* *
3089815 GACCGCAATAGCTTCCGTTATGCCTGTAATCACGATAAACGTAACGTGATCGAAATAC
1 GACCGCAATAGCTTCCGTTATGCCTGCAATCACGATAAACATAACGTGATCGAAATAC
3089873 GACCGCAATAGC
1 GACCGCAATAGC
3089885 AATTTAAATC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (58 bp):
GACCGCAATAGCTTCCGTTATGCCTGCAATCACGATAAACATAACGTGATCGAAATAC
Found at i:3090928 original size:21 final size:21
Alignment explanation
Indices: 3090889--3090928 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3090879 TAATTATTAA
*
3090889 AAAAATAAAAATTTACTTTAC
1 AAAAATAAAAATGTACTTTAC
3090910 AAAAATAAAATATGT-CTTT
1 AAAAATAAAA-ATGTACTTT
3090929 CCTCTCACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (21 bp):
AAAAATAAAAATGTACTTTAC
Found at i:3097433 original size:25 final size:26
Alignment explanation
Indices: 3097394--3097445 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
3097384 TAGAATATAT
3097394 TTTATTATTTATTATAT-TATATTAA
1 TTTATTATTTATTATATATATATTAA
*
3097419 TTTATTATGTT-TTATATATATCTTAA
1 TTTATTAT-TTATTATATATATATTAA
3097445 T
1 T
3097446 AGGGTATGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTATTATTTATTATATATATATTAA
Found at i:3104055 original size:22 final size:20
Alignment explanation
Indices: 3104009--3104049 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
3103999 ATTTTCAATG
*
3104009 ATTTATTGAAATTAATTTAATA
1 ATTTATTG--ATTAATTGAATA
3104031 ATTTATTGATTAATTGAAT
1 ATTTATTGATTAATTGAAT
3104050 TAAATTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (20 bp):
ATTTATTGATTAATTGAATA
Found at i:3104058 original size:18 final size:18
Alignment explanation
Indices: 3104035--3104070 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3104025 TTAATAATTT
3104035 ATTGATT-AATTGAATTAA
1 ATTGATTGAATTG-ATTAA
3104053 ATTGATTGAATTGATTAA
1 ATTGATTGAATTGATTAA
3104071 TTCAATAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (18 bp):
ATTGATTGAATTGATTAA
Found at i:3111255 original size:2 final size:2
Alignment explanation
Indices: 3111248--3111272 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3111238 TTCCGTAGAT
3111248 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3111273 TTTTCTCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3114958 original size:15 final size:15
Alignment explanation
Indices: 3114938--3114968 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3114928 AATTCCCCTC
3114938 AGAAAAGAAAAAGAA
1 AGAAAAGAAAAAGAA
3114953 AGAAAAGAAAAAGAA
1 AGAAAAGAAAAAGAA
3114968 A
1 A
3114969 AAACTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAAAGAA
Found at i:3116509 original size:32 final size:32
Alignment explanation
Indices: 3116443--3116540 Score: 92
Period size: 32 Copynumber: 3.1 Consensus size: 32
3116433 TAGATTTAAT
* ** *
3116443 AATTTATATATTTACATTATATAAAATATTAA
1 AATTTATATATTTAAATTATATTTAATATAAA
* *
3116475 AATTTATATATTTATATTATATTTTATATAAA
1 AATTTATATATTTAAATTATATTTAATATAAA
* * *
3116507 AA-TTATACATTAAAATT-TATATTGATATAAA
1 AATTTATATATTTAAATTATAT-TTAATATAAA
3116538 AAT
1 AAT
3116541 ATAAAAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 3 0.05
31 23 0.42
32 29 0.53
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (32 bp):
AATTTATATATTTAAATTATATTTAATATAAA
Found at i:3116622 original size:16 final size:15
Alignment explanation
Indices: 3116598--3116627 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3116588 TTTTACATCG
3116598 TTTTAATTTTATTTT
1 TTTTAATTTTATTTT
3116613 TTTTATATTTTATTT
1 TTTTA-ATTTTATTT
3116628 ATATTATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTAATTTTATTTT
Found at i:3116634 original size:16 final size:16
Alignment explanation
Indices: 3116603--3116636 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3116593 CATCGTTTTA
* *
3116603 ATTTTATTTTTTTTAT
1 ATTTTATTTATATTAT
3116619 ATTTTATTTATATTAT
1 ATTTTATTTATATTAT
3116635 AT
1 AT
3116637 CATATATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTATTTATATTAT
Found at i:3135650 original size:18 final size:18
Alignment explanation
Indices: 3135608--3135657 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
3135598 TTTTTTTAAC
3135608 TTAAATA-T-AAAA-TTA
1 TTAAATATTAAAAATTTA
* *
3135623 TAAAAAATTAAAAATTTA
1 TTAAATATTAAAAATTTA
3135641 TTAAATATTAAACAATT
1 TTAAATATTAAA-AATT
3135658 CACTTTAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 5 0.19
16 1 0.04
17 4 0.15
18 13 0.48
19 4 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAATATTAAAAATTTA
Found at i:3140166 original size:3 final size:3
Alignment explanation
Indices: 3140158--3140187 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3140148 CGAAATTGAA
*
3140158 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3140188 TTCCCTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3153780 original size:10 final size:10
Alignment explanation
Indices: 3153767--3153871 Score: 74
Period size: 10 Copynumber: 10.2 Consensus size: 10
3153757 CAGATGAGAG
3153767 AAAATGAAAA
1 AAAATGAAAA
3153777 AAAATGAAAA
1 AAAATGAAAA
3153787 ATAAA--AAAA
1 A-AAATGAAAA
**
3153796 TAAAAAAATAAA
1 -AAAATGA-AAA
3153808 AAAAT-AAAA
1 AAAATGAAAA
3153817 AAAATGAAAA
1 AAAATGAAAA
*
3153827 AATGAAAGAAAA
1 AA--AATGAAAA
*
3153839 AATAA-GAGAA
1 AA-AATGAAAA
*
3153849 AAAATAAGAAA
1 AAAATGA-AAA
3153860 AAAATGAAAA
1 AAAATGAAAA
3153870 AA
1 AA
3153872 GAAAAGAAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
9 17 0.22
10 31 0.40
11 18 0.23
12 12 0.15
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.10
Consensus pattern (10 bp):
AAAATGAAAA
Found at i:3153786 original size:8 final size:8
Alignment explanation
Indices: 3153775--3153876 Score: 70
Period size: 8 Copynumber: 12.5 Consensus size: 8
3153765 AGAAAATGAA
3153775 AAAAAATG
1 AAAAAATG
*
3153783 -AAAAATA
1 AAAAAATG
*
3153790 AAAAAATA
1 AAAAAATG
*
3153798 AAAAAATA
1 AAAAAATG
*
3153806 AAAAAATAA
1 AAAAAAT-G
3153815 AAAAAATG
1 AAAAAATG
3153823 AAAAAATG
1 AAAAAATG
3153831 AAAGAAA--
1 AAA-AAATG
3153838 AAATAAGA-G
1 AAA-AA-ATG
3153847 AAAAAATAAG
1 AAAAAAT--G
3153857 AAAAAAATG
1 -AAAAAATG
3153866 AAAAAA-G
1 AAAAAATG
3153873 AAAA
1 AAAA
3153877 GAAAAACTCA
Statistics
Matches: 82, Mismatches: 3, Indels: 19
0.79 0.03 0.18
Matches are distributed among these distances:
7 17 0.21
8 42 0.51
9 15 0.18
10 1 0.01
11 7 0.09
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:3153812 original size:41 final size:40
Alignment explanation
Indices: 3153762--3153870 Score: 121
Period size: 41 Copynumber: 2.6 Consensus size: 40
3153752 TGGGTCAGAT
*
3153762 GAGAGAAAATGAAAAAAAATGAAAAATAAAAAAATAAAAAAA
1 GAGAAAAAAT-AAAAAAAATGAAAAATAAAAAAA-AAAAAAA
* * * *
3153804 TA-AAAAAATAAAAAAAATGAAAAAATGAAAGAAAAAATAA
1 GAGAAAAAATAAAAAAAATG-AAAAATAAAAAAAAAAAAAA
3153844 GAGAAAAAATAAGAAAAAAATGAAAAA
1 GAGAAAAAAT-A-AAAAAAATGAAAAA
3153871 AGAAAAGAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
40 17 0.30
41 24 0.42
42 7 0.12
43 9 0.16
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (40 bp):
GAGAAAAAATAAAAAAAATGAAAAATAAAAAAAAAAAAAA
Found at i:3153828 original size:12 final size:11
Alignment explanation
Indices: 3153773--3153882 Score: 78
Period size: 12 Copynumber: 9.3 Consensus size: 11
3153763 AGAGAAAATG
3153773 AAAAAAAATGAA
1 AAAAAAAAT-AA
3153785 AAATAAAAA-AA
1 AAA-AAAAATAA
*
3153796 TAAAAAAATAA
1 AAAAAAAATAA
*
3153807 AAAAATAAAAAA
1 AAAAA-AAATAA
3153819 AATGAAAAAATGAA
1 AA--AAAAAAT-AA
*
3153833 AGAAAAAATAA
1 AAAAAAAATAA
*
3153844 GAGAAAAAATAA
1 -AAAAAAAATAA
*
3153856 GAAAAAAATGAA
1 AAAAAAAAT-AA
*
3153868 AAAAGAAAAGAA
1 AAAA-AAAATAA
3153880 AAA
1 AAA
3153883 CTCAAATTGA
Statistics
Matches: 80, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
10 5 0.06
11 19 0.24
12 38 0.47
13 12 0.15
14 6 0.08
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:3154945 original size:21 final size:21
Alignment explanation
Indices: 3154921--3155092 Score: 83
Period size: 21 Copynumber: 7.8 Consensus size: 21
3154911 ATTATGAATA
* *
3154921 TTTTGATGAGAATTTTTGAGT
1 TTTTAATGAGAATCTTTGAGT
*
3154942 TTTTAAATGAAAATCTTTGAGT
1 TTTT-AATGAGAATCTTTGAGT
* *
3154964 TTTAAATGAGAATCTTTAAGACAT
1 TTTTAATGAGAATCTTT--GA-GT
** * *
3154988 TTCAAATAAAAATCTTTGAGT
1 TTTTAATGAGAATCTTTGAGT
* * * *
3155009 CTTAAATGAAAATCTTTAAGAT
1 TTTTAATGAGAATCTTTGAG-T
* * *
3155031 ATCTTCAAATAAGAATATTTGAGT
1 -T-TT-TAATGAGAATCTTTGAGT
** *
3155055 TTCAAATGAGAATCTTTGAAT
1 TTTTAATGAGAATCTTTGAGT
**
3155076 TTCAAATGAGAATCTTT
1 TTTTAATGAGAATCTTT
3155093 AAGGTGTGAA
Statistics
Matches: 120, Mismatches: 23, Indels: 16
0.75 0.14 0.10
Matches are distributed among these distances:
21 65 0.54
22 21 0.17
23 3 0.03
24 18 0.15
25 13 0.11
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (21 bp):
TTTTAATGAGAATCTTTGAGT
Found at i:3155003 original size:45 final size:44
Alignment explanation
Indices: 3154946--3155092 Score: 181
Period size: 45 Copynumber: 3.3 Consensus size: 44
3154936 TTGAGTTTTT
*
3154946 AAATGAAAATCTTTGAGTTTTAAATGAGAATCTTTAAGACATTTC
1 AAATAAAAATCTTTGAGTTTTAAATGAGAATCTTTAAGA-ATTTC
* *
3154991 AAATAAAAATCTTTGAGTCTTAAATGAAAATCTTTAAGATATCTTC
1 AAATAAAAATCTTTGAGTTTTAAATGAGAATCTTTAAGA-AT-TTC
* * *
3155037 AAATAAGAATATTTGAGTTTCAAATGAGAATCTTT--GAATTTC
1 AAATAAAAATCTTTGAGTTTTAAATGAGAATCTTTAAGAATTTC
* *
3155079 AAATGAGAATCTTT
1 AAATAAAAATCTTT
3155093 AAGGTGTGAA
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
42 15 0.17
43 2 0.02
44 2 0.02
45 38 0.42
46 33 0.37
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37
Consensus pattern (44 bp):
AAATAAAAATCTTTGAGTTTTAAATGAGAATCTTTAAGAATTTC
Found at i:3155069 original size:67 final size:64
Alignment explanation
Indices: 3154926--3155095 Score: 164
Period size: 67 Copynumber: 2.5 Consensus size: 64
3154916 GAATATTTTG
* * * *
3154926 ATGAGAATTTTTGAGTTTTTAAATGAAAATCTTTGAGTTTTAAATGAGAATCTTTAAGACATTTC
1 ATGAGAATCTTTGAG--TTTAAATGAAAATCTTTAAGTTTTAAATAAGAATATTT-AGACATTTC
3154991 AA
63 AA
* * *
3154993 ATAAAAATCTTTGAGTCTTAAATGAAAATCTTTAAGATATCTTCAAATAAGAATATTT-GA-GTT
1 ATGAGAATCTTTGAGT-TTAAATGAAAATCTTTAAG-T-T-TT-AAATAAGAATATTTAGACATT
3155056 TCAA
61 TCAA
* *
3155060 ATGAGAATCTTTGAATTTCAAATGAGAATCTTTAAG
1 ATGAGAATCTTTGAGTTT-AAATGAAAATCTTTAAG
3155096 GTGTGAAACC
Statistics
Matches: 86, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
65 1 0.01
66 20 0.23
67 48 0.56
68 3 0.03
69 2 0.02
70 12 0.14
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.39
Consensus pattern (64 bp):
ATGAGAATCTTTGAGTTTAAATGAAAATCTTTAAGTTTTAAATAAGAATATTTAGACATTTCAA
Found at i:3155180 original size:80 final size:80
Alignment explanation
Indices: 3155056--3155304 Score: 223
Period size: 73 Copynumber: 3.2 Consensus size: 80
3155046 TATTTGAGTT
* * * *
3155056 TCAAATGAGAATCTTTGAA-TTTC-AAATGAGAATCTTTAAGGTGTGAAACCCAAAATTTATCGA
1 TCAAATGAAAAT-TTTTAAGTTTCAAAATAAGAATCTTTGAGGTGTGAAACCCAAAATTTATCGA
*
3155119 ATGTGAATCTTCGAAT
65 ATGTGAATCTTCGAAC
****
3155135 TCAAATGAAAATTTTTAAGTTTCAAAATAAGAATCTTTGAGGTGTGAAGTTTAAAA--T-T----
1 TCAAATGAAAATTTTTAAGTTTCAAAATAAGAATCTTTGAGGTGTGAAACCCAAAATTTATCGAA
* *
3155193 TGTCAATCTTCAAAC
66 TGTGAATCTTCGAAC
* * * * *
3155208 TCAAAT-AAGAATCTTTAGGTTTCAAAATAAAAATCTTTGAGGTGTGAAACCCTAAAGTTCATCG
1 TCAAATGAA-AATTTTTAAGTTTCAAAATAAGAATCTTTGAGGTGTGAAACCC-AAAATTTATCG
*
3155272 AATATGAATCTTCGAAC
64 AATGTGAATCTTCGAAC
*
3155289 T-AGAATGAAAAGTTTT
1 TCA-AATGAAAATTTTT
3155305 GAACTTTTGG
Statistics
Matches: 132, Mismatches: 25, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
72 2 0.02
73 54 0.41
74 3 0.02
77 2 0.02
78 6 0.05
79 15 0.11
80 27 0.20
81 21 0.16
82 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (80 bp):
TCAAATGAAAATTTTTAAGTTTCAAAATAAGAATCTTTGAGGTGTGAAACCCAAAATTTATCGAA
TGTGAATCTTCGAAC
Found at i:3155683 original size:114 final size:114
Alignment explanation
Indices: 3155553--3156022 Score: 678
Period size: 114 Copynumber: 4.1 Consensus size: 114
3155543 GAATTTGAGT
*
3155553 GAAAAGCTTTGAACTCAACTTTTGGATGCAAATCTCTAAATTTTTGAGTGAGAACCTTTGAACTT
1 GAAAAGCTTTGAACTCAACTTTTGGATGCAAATCTCTAAATTTTTGAATGAGAACCTTTGAACTT
* * * *
3155618 AGATGTGAAGCTCTAAGATTTCTTGAATGT-AAACTTTCAAAATTCAAAT
66 AGATGTGAAACTCTAAGATTTCTTGAATGTGAATCTCT-AAAATTCAAAC
* * ** *
3155667 GAAAAGCTTTAAACTCAATTTTTGGATGTGAATCTCTAAATTTTTTAATGAGAACCTTTGAACTT
1 GAAAAGCTTTGAACTCAACTTTTGGATGCAAATCTCTAAATTTTTGAATGAGAACCTTTGAACTT
*
3155732 AGATGT-AGAACTCTAAGATTTCTTGGATGTGAATCTCTAAAATTCAAAC
66 AGATGTGA-AACTCTAAGATTTCTTGAATGTGAATCTCTAAAATTCAAAC
* * * * *
3155781 AAAAAGCTTTGAACTTAACTTTTGG-TGCGAATCTCTAAAATTTTGAGTGAGAACCTTTGAACTT
1 GAAAAGCTTTGAACTCAACTTTTGGATGCAAATCTCTAAATTTTTGAATGAGAACCTTTGAACTT
*
3155845 AGATGTGAAACTCTAAGATTTCTTGAATGTGAACCT-TCAAAATTCAAAC
66 AGATGTGAAACTCTAAGATTTCTTGAATGTGAATCTCT-AAAATTCAAAC
* * *
3155894 GAAAAGCTTTGAACTCAACTTTTGGATGCAAATTTTTAAATTTTTGAATGAGAACCTTCGAACTT
1 GAAAAGCTTTGAACTCAACTTTTGGATGCAAATCTCTAAATTTTTGAATGAGAACCTTTGAACTT
* *
3155959 AGATGTAAAACTTTAAGATTTCTTGAATGTGAATCTCTAAAATTCAAAC
66 AGATGTGAAACTCTAAGATTTCTTGAATGTGAATCTCTAAAATTCAAAC
*
3156008 GAAAAACTTTGAACT
1 GAAAAGCTTTGAACT
3156023 TTTGGGATGT
Statistics
Matches: 317, Mismatches: 33, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
112 1 0.00
113 102 0.32
114 208 0.66
115 6 0.02
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (114 bp):
GAAAAGCTTTGAACTCAACTTTTGGATGCAAATCTCTAAATTTTTGAATGAGAACCTTTGAACTT
AGATGTGAAACTCTAAGATTTCTTGAATGTGAATCTCTAAAATTCAAAC
Found at i:3155708 original size:22 final size:22
Alignment explanation
Indices: 3155683--3155772 Score: 60
Period size: 22 Copynumber: 4.1 Consensus size: 22
3155673 CTTTAAACTC
3155683 AATTTTTGGATGTGAATCTCTA
1 AATTTTTGGATGTGAATCTCTA
** * * * *
3155705 AATTTTTTAATGAGAACCTTTG
1 AATTTTTGGATGTGAATCTCTA
* *
3155727 AA--CTTAGATGTAGAA-CTCTA
1 AATTTTTGGATGT-GAATCTCTA
3155747 AGATTTCTTGGATGTGAATCTCTA
1 A-ATTT-TTGGATGTGAATCTCTA
3155771 AA
1 AA
3155773 ATTCAAACAA
Statistics
Matches: 48, Mismatches: 14, Indels: 11
0.66 0.19 0.15
Matches are distributed among these distances:
20 9 0.19
21 4 0.08
22 18 0.38
23 4 0.08
24 13 0.27
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (22 bp):
AATTTTTGGATGTGAATCTCTA
Found at i:3155827 original size:227 final size:229
Alignment explanation
Indices: 3155554--3156023 Score: 757
Period size: 227 Copynumber: 2.1 Consensus size: 229
3155544 AATTTGAGTG
* *
3155554 AAAAGCTTTGAACTCAACTTTTGGATGCAAATCTCTAAATTTTTGAGTGAGAACCTTTGAACTTA
1 AAAAGCTTTGAACTTAACTTTTGGATGCAAATCTCTAAAATTTTGAGTGAGAACCTTTGAACTTA
* * *
3155619 GATGTGAAGCTCTAAGATTTCTTGAATGTAAACTTTCAAAATTCAAATGAAAAGCTTTAAACTCA
66 GATGTGAAACTCTAAGATTTCTTGAATGTAAACCTTCAAAATTCAAACGAAAAGCTTTAAACTCA
* ** * * *
3155684 ATTTTTGGATGTGAATCTCTAAATTTTTTAATGAGAACCTTTGAACTTAGATGTAGAACTCTAAG
131 ACTTTTGGATGCAAATCTCTAAATTTTTGAATGAGAACCTTCGAACTTAGATGTAAAACTCTAAG
*
3155749 ATTTCTTGGATGTGAATCTCTAAAATTCAAAC-A
196 ATTTCTTGAATGTGAATCTCTAAAATTCAAACGA
*
3155782 AAAAGCTTTGAACTTAACTTTTGG-TGCGAATCTCTAAAATTTTGAGTGAGAACCTTTGAACTTA
1 AAAAGCTTTGAACTTAACTTTTGGATGCAAATCTCTAAAATTTTGAGTGAGAACCTTTGAACTTA
* *
3155846 GATGTGAAACTCTAAGATTTCTTGAATGTGAACCTTCAAAATTCAAACGAAAAGCTTTGAACTCA
66 GATGTGAAACTCTAAGATTTCTTGAATGTAAACCTTCAAAATTCAAACGAAAAGCTTTAAACTCA
* * *
3155911 ACTTTTGGATGCAAATTTTTAAATTTTTGAATGAGAACCTTCGAACTTAGATGTAAAACTTTAAG
131 ACTTTTGGATGCAAATCTCTAAATTTTTGAATGAGAACCTTCGAACTTAGATGTAAAACTCTAAG
3155976 ATTTCTTGAATGTGAATCTCTAAAATTCAAACGA
196 ATTTCTTGAATGTGAATCTCTAAAATTCAAACGA
3156010 AAAA-CTTTGAACTT
1 AAAAGCTTTGAACTT
3156024 TTGGGATGTG
Statistics
Matches: 223, Mismatches: 18, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
227 195 0.87
228 28 0.13
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (229 bp):
AAAAGCTTTGAACTTAACTTTTGGATGCAAATCTCTAAAATTTTGAGTGAGAACCTTTGAACTTA
GATGTGAAACTCTAAGATTTCTTGAATGTAAACCTTCAAAATTCAAACGAAAAGCTTTAAACTCA
ACTTTTGGATGCAAATCTCTAAATTTTTGAATGAGAACCTTCGAACTTAGATGTAAAACTCTAAG
ATTTCTTGAATGTGAATCTCTAAAATTCAAACGA
Found at i:3156952 original size:20 final size:19
Alignment explanation
Indices: 3156908--3156953 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3156898 ATTCCAGCCA
*
3156908 AATTTTTCGATGGCGATTG
1 AATTTTTCGACGGCGATTG
* *
3156927 AATTTTTCGACGTCGGTTG
1 AATTTTTCGACGGCGATTG
*
3156946 AACTTTTC
1 AATTTTTC
3156954 AGTGTGTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (19 bp):
AATTTTTCGACGGCGATTG
Found at i:3157396 original size:4 final size:4
Alignment explanation
Indices: 3157389--3157434 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
3157379 TTTTTTCTTC
* *
3157389 ATTT ATTT ATTT ATTT ATTT ATTT -TTT TTTT ACTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
3157435 GATTAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:3157499 original size:10 final size:10
Alignment explanation
Indices: 3157474--3157521 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 10
3157464 AATTTTAATG
3157474 TTAATTTTAGTT
1 TTAA-TTTA-TT
3157486 TTAATTTATT
1 TTAATTTATT
3157496 TTAATTTATT
1 TTAATTTATT
3157506 TTATTATTT-TT
1 TTA--ATTTATT
3157517 TTAAT
1 TTAAT
3157522 GATATTCCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 2 0.06
10 15 0.44
11 9 0.26
12 8 0.24
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (10 bp):
TTAATTTATT
Found at i:3157502 original size:6 final size:6
Alignment explanation
Indices: 3157462--3157502 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
3157452 TTGATATTCC
* *
3157462 TTAATT TTAATG TTAATT TTAGTT TTAA-T TT-ATT TTAATT T
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT T
3157503 ATTTTATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
4 1 0.03
5 6 0.21
6 22 0.76
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (6 bp):
TTAATT
Found at i:3157652 original size:71 final size:72
Alignment explanation
Indices: 3157529--3157669 Score: 180
Period size: 71 Copynumber: 2.0 Consensus size: 72
3157519 AATGATATTC
* * **
3157529 CTAAAATAAAATTTTCAAAAAAATGTTTATGAGGAAAAGTTGAAAATATCAATTTTTCTTAAAAA
1 CTAAAATAAAATTTTC-AAAAAATATTTATGAGGAAAAATTGAAAATATCAATTTCCCTTAAAAA
3157594 TAAAATTT
65 TAAAATTT
* *
3157602 CTAAAATAAAAATTTTC-AAAAGTATTT-TG-GGAAAAAATTGAAAGTATCAATTTCCCTTAAAA
1 CTAAAAT-AAAATTTTCAAAAAATATTTATGAGG-AAAAATTGAAAATATCAATTTCCCTTAAAA
3157664 ATAAAA
64 ATAAAA
3157670 AGGTTTTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
70 2 0.03
71 34 0.57
72 8 0.13
73 7 0.12
74 9 0.15
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (72 bp):
CTAAAATAAAATTTTCAAAAAATATTTATGAGGAAAAATTGAAAATATCAATTTCCCTTAAAAAT
AAAATTT
Found at i:3157737 original size:53 final size:55
Alignment explanation
Indices: 3157679--3157830 Score: 191
Period size: 53 Copynumber: 2.7 Consensus size: 55
3157669 AAGGTTTTTT
* *
3157679 AAAAAATATTTTTAAGGAAAAGTTGAAAATATCAATTTTCCTTGAAATT-CA-AGA
1 AAAAAATA-TTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAATAGA
* *
3157733 AAAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAATTTCAGAA
1 AAAAAATATTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATT-AAA--T-AG-A
*
3157793 AAAAAATATTTTAAAGAAAAGTTGAAAGTATCAATTTT
1 AAAAAATATTTTAAGGAAAAGTTGAAAGTATCAATTTT
3157831 TCTTACAAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
53 37 0.44
54 8 0.09
55 1 0.01
59 2 0.02
60 37 0.44
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (55 bp):
AAAAAATATTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAATAGA
Found at i:3157743 original size:115 final size:113
Alignment explanation
Indices: 3157619--3157830 Score: 266
Period size: 115 Copynumber: 1.9 Consensus size: 113
3157609 AAAAATTTTC
* ***
3157619 AAAAGTATTTTG-GGAAAAAATTGAAAGTATCAATTTCCCTTAAAAATAAAAAGGTTTTTTAAAA
1 AAAAATATTTTGAGG-AAAAATTGAAAGTATCAATTTCCCTT-AAAATAAAAA--TTTCAGAAAA
* *
3157683 AATAT-TTTTAAGGAAAAGTTGAAAATATCAATTTTCCTTGAAATTCAAGAA
62 AAAATATTTTAAAGAAAAGTTGAAAATATCAATTTTCCTTGAAATTCAAGAA
* ** * *
3157734 AAAAATATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAATTTCAGAAAAAAAA
1 AAAAATATTTTGAGGAAAAATTGAAAGTATCAATTTCCCTTAAAATAAAAATTTCAGAAAAAAAA
*
3157799 TATTTTAAAGAAAAGTTGAAAGTATCAATTTT
66 TATTTTAAAGAAAAGTTGAAAATATCAATTTT
3157831 TCTTACAAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
112 11 0.13
113 28 0.34
114 8 0.10
115 34 0.41
116 2 0.02
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (113 bp):
AAAAATATTTTGAGGAAAAATTGAAAGTATCAATTTCCCTTAAAATAAAAATTTCAGAAAAAAAA
TATTTTAAAGAAAAGTTGAAAATATCAATTTTCCTTGAAATTCAAGAA
Found at i:3160444 original size:2 final size:2
Alignment explanation
Indices: 3160402--3160431 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3160392 ACATTTTACC
3160402 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3160432 CACATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3162832 original size:27 final size:29
Alignment explanation
Indices: 3162744--3162832 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 29
3162734 GTTAATGGTC
* * *
3162744 TTTAAATTATAATTAAAATATTTAGTGTAATA
1 TTTAAATTAT-A--AAAATTTTTAATATAATA
* * *
3162776 TTTAAATTTTAAAAATTTTTGATATGATA
1 TTTAAATTATAAAAATTTTTAATATAATA
*
3162805 TTTAAATTAT-AAATTTTTTAAT-TAATA
1 TTTAAATTATAAAAATTTTTAATATAATA
3162832 T
1 T
3162833 AATACTTGAA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
27 5 0.11
28 10 0.21
29 22 0.47
31 1 0.02
32 9 0.19
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
TTTAAATTATAAAAATTTTTAATATAATA
Found at i:3176428 original size:17 final size:17
Alignment explanation
Indices: 3176398--3176430 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3176388 AAAATAAAAA
3176398 TTTATTTAATAATATTT
1 TTTATTTAATAATATTT
3176415 TTTATGTTAA-AATATT
1 TTTAT-TTAATAATATT
3176431 AATATATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTATTTAATAATATTT
Found at i:3176456 original size:16 final size:16
Alignment explanation
Indices: 3176423--3176469 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
3176413 TTTTTATGTT
3176423 AAAATATTAATATATTC
1 AAAATATTAATAT-TTC
*
3176440 ACAAT-TTAAATATTTC
1 AAAATATT-AATATTTC
3176456 AAAATATTAATATT
1 AAAATATTAATATT
3176470 ACTTATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATATTAATATTTC
Found at i:3180802 original size:15 final size:14
Alignment explanation
Indices: 3180756--3180808 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
3180746 TCGTATTTAA
3180756 TAATTTTAAATAAAT
1 TAATTTTAAAT-AAT
* *
3180771 TGAATGTTAAATGAT
1 T-AATTTTAAATAAT
3180786 TAATTTTAAAATAAT
1 TAATTTT-AAATAAT
3180801 T-ATTTTAA
1 TAATTTTAA
3180809 TTGGATGTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 2 0.06
14 10 0.31
15 11 0.34
16 9 0.28
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (14 bp):
TAATTTTAAATAAT
Found at i:3192422 original size:3 final size:3
Alignment explanation
Indices: 3192408--3192479 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
3192398 AGATGCTTTC
* * * *
3192408 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT TTT ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
3192456 TTT ATT ATT ATCT -TT ATT TTT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT
3192480 TTTTTGTTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 1 0.02
3 55 0.96
4 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:3192504 original size:21 final size:21
Alignment explanation
Indices: 3192478--3192517 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3192468 TTTATTTTTA
3192478 TTTTTTTGTTTCCTTTTCTGT
1 TTTTTTTGTTTCCTTTTCTGT
*
3192499 TTTTTTTTTTTCCTTTTCT
1 TTTTTTTGTTTCCTTTTCT
3192518 TTTGATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTTTTGTTTCCTTTTCTGT
Found at i:3192861 original size:20 final size:21
Alignment explanation
Indices: 3192838--3192880 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
3192828 GGTTCTATGA
*
3192838 GTGAATTCAGGTTTAT-GAAG
1 GTGAATTCAGGATTATAGAAG
*
3192858 GTGAATTTAGGATTATAGAAG
1 GTGAATTCAGGATTATAGAAG
3192879 GT
1 GT
3192881 TTGGGGAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (21 bp):
GTGAATTCAGGATTATAGAAG
Found at i:3204838 original size:118 final size:118
Alignment explanation
Indices: 3204628--3205019 Score: 430
Period size: 118 Copynumber: 3.3 Consensus size: 118
3204618 GCCTCGATTA
* * * * * *
3204628 CTTGATCTTGGCTTAGTCTAGATCATCTC-TATTGATTCATGGTTTCATCTTGATTATTTATTTT
1 CTTGATCTTGGCTCAGTCCAGATCATTTCTTA-TGATTCATGATTTTATCCTGATTATTTATTTT
* * ** * ** * *
3204692 CAACCTCGATTCGATCTTGGTTGTCTCATTTGACTCGTGGTTTTATCCCAGTCG
65 CGACCTCGACTCGATCTTGGTCATCTCATTTGACTCATAATTTTATCTCAGTTG
* ** * *
3204746 CTTGATCTTGGCTCAGTCCAGATCATTCCTTATGATTCATGATTTTATCCCAATCATTTATTCTC
1 CTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGATTTTATCCTGATTATTTATTTTC
* * *
3204811 GACCTCGACTCGATCTTGGTCACCTCATTTGATTCATAATTTTATCTCGGTTG
66 GACCTCGACTCGATCTTGGTCATCTCATTTGACTCATAATTTTATCTCAGTTG
* * *
3204864 CTTGATTTTGGCTCAGTCTAGATCATTTTTTATGATTCATGATTCCTT-T-CTGATTATTTATTT
1 CTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGATT--TTATCCTGATTATTTATTT
* * * * *
3204927 TTGACCTCGACTTGGTCCTGGTCATCTCATTTGACTCATAATTTTGTCTCAGTTG
64 TCGACCTCGACTCGATCTTGGTCATCTCATTTGACTCATAATTTTATCTCAGTTG
* * *
3204982 TTTGATCTTGGCTCAGTCCAAATCATTTTTTATGATTC
1 CTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTC
3205020 GTGGTTCCGT
Statistics
Matches: 228, Mismatches: 43, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
118 223 0.98
119 3 0.01
120 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (118 bp):
CTTGATCTTGGCTCAGTCCAGATCATTTCTTATGATTCATGATTTTATCCTGATTATTTATTTTC
GACCTCGACTCGATCTTGGTCATCTCATTTGACTCATAATTTTATCTCAGTTG
Found at i:3205060 original size:236 final size:236
Alignment explanation
Indices: 3204628--3205063 Score: 509
Period size: 236 Copynumber: 1.8 Consensus size: 236
3204618 GCCTCGATTA
* * *
3204628 CTTGATCTTGGCTTAGTCTAGATCATCTCTATTGATTCATGGTTTCATCTTGATTATTTATTTTC
1 CTTGATCTTGGCTCAGTCTAGATCATCTCTATTGATTCATGATTCCATCTTGATTATTTATTTTC
* ** * **
3204693 AACCTCGATTCGATCTTGGTTGTCTCATTTGACTCGTGGTTTTATCCCAGTCGCTTGATCTTGGC
66 AACCTCGATTCGATCCTGGTCATCTCATTTGACTCATAATTTTATCCCAGTCGCTTGATCTTGGC
* ** * *
3204758 TCAGTCCAGATCATTCCTTATGATTCATGATTTTATCCCAATCATTTATTCTCGACCTCGACTCG
131 TCAGTCCAAATCATTCCTTATGATTCATGATTCCATCCCAATCATTTATTCTCAACCTCAACTCG
3204823 ATCTTGGTCACCTCATTTGATTCATAATTTTATCTCGGTTG
196 ATCTTGGTCACCTCATTTGATTCATAATTTTATCTCGGTTG
* * * *
3204864 CTTGATTTTGGCTCAGTCTAGATCAT-TTTTTATGATTCATGATTCC-TTTCTGATTATTTATTT
1 CTTGATCTTGGCTCAGTCTAGATCATCTCTAT-TGATTCATGATTCCATCT-TGATTATTTATTT
** * * * * *
3204927 TTGACCTCGACTT-GGTCCTGGTCATCTCATTTGACTCATAATTTTGTCTCAGTTGTTTGATCTT
64 TCAACCTCGA-TTCGATCCTGGTCATCTCATTTGACTCATAATTTTATCCCAGTCGCTTGATCTT
** * * * * * ** *
3204991 GGCTCAGTCCAAATCATTTTTTATGATTCGTGGTTCCGTCTCGATCATTTATTCTCAATTTTAAC
128 GGCTCAGTCCAAATCATTCCTTATGATTCATGATTCCATCCCAATCATTTATTCTCAACCTCAAC
3205056 TCGATCTT
193 TCGATCTT
3205064 AGTCGTTTTA
Statistics
Matches: 162, Mismatches: 35, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
235 5 0.03
236 155 0.96
237 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (236 bp):
CTTGATCTTGGCTCAGTCTAGATCATCTCTATTGATTCATGATTCCATCTTGATTATTTATTTTC
AACCTCGATTCGATCCTGGTCATCTCATTTGACTCATAATTTTATCCCAGTCGCTTGATCTTGGC
TCAGTCCAAATCATTCCTTATGATTCATGATTCCATCCCAATCATTTATTCTCAACCTCAACTCG
ATCTTGGTCACCTCATTTGATTCATAATTTTATCTCGGTTG
Found at i:3205371 original size:26 final size:26
Alignment explanation
Indices: 3205326--3205396 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
3205316 AAGACAGTTG
* *
3205326 TAGACACCTATTTTGGTCCGGA-TCCAAT
1 TAGAC-CC-ATTTTGATCCGGACT-CAAC
*
3205354 TAGGCCCATTTTGATCCGGACTCAAC
1 TAGACCCATTTTGATCCGGACTCAAC
3205380 TAGACCCATTTTGATCC
1 TAGACCCATTTTGATCC
3205397 AAGCCCGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 31 0.82
27 3 0.08
28 4 0.11
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (26 bp):
TAGACCCATTTTGATCCGGACTCAAC
Found at i:3205516 original size:3 final size:3
Alignment explanation
Indices: 3205502--3205581 Score: 71
Period size: 3 Copynumber: 28.0 Consensus size: 3
3205492 AGATACTTTC
* * * *
3205502 ATT ATC ATT ATT ATT ATT ATT ACT ATT TTT ATT -TT -TT ATT TTT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
3205547 ATT ATT A-T ATT ATT ATT ATT ATCT -TT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
3205582 TTTTTTGTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
2 9 0.15
3 52 0.84
4 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:3206127 original size:19 final size:19
Alignment explanation
Indices: 3206103--3206145 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3206093 CCAACAAGAT
3206103 TCCGACGAGATTTTT-AGAA
1 TCCGAC-AGATTTTTCAGAA
*
3206122 TCCGACAGGTTTTTCAGAA
1 TCCGACAGATTTTTCAGAA
*
3206141 ACCGA
1 TCCGA
3206146 TGGGTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (19 bp):
TCCGACAGATTTTTCAGAA
Found at i:3206237 original size:51 final size:51
Alignment explanation
Indices: 3206147--3206247 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 51
3206137 AGAAACCGAT
* * * *
3206147 GGGTTTTCAATTTTTGATTGAATTTTTTGACGAAATTTCTAGAAATAGGTG
1 GGGTTTTCAATTTTTAATTAAATTTTTAGACGAAATTTCTAGAAAGAGGTG
* * *
3206198 GGGTTTTCAATTTTTAATTAAATTTTTCAG-TGGACTTTCTAGAAAGAGGT
1 GGGTTTTCAATTTTTAATTAAATTTTT-AGACGAAATTTCTAGAAAGAGGT
3206248 CAGAGGTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (51 bp):
GGGTTTTCAATTTTTAATTAAATTTTTAGACGAAATTTCTAGAAAGAGGTG
Found at i:3206442 original size:20 final size:20
Alignment explanation
Indices: 3206417--3206458 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3206407 TGATCGTGGG
3206417 TTTTTTT-TTTCATTTTTATT
1 TTTTTTTATTTCA-TTTTATT
*
3206437 TTTTTTTATTTGATTTTATT
1 TTTTTTTATTTCATTTTATT
3206457 TT
1 TT
3206459 ATTTCTAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (20 bp):
TTTTTTTATTTCATTTTATT
Found at i:3206452 original size:15 final size:15
Alignment explanation
Indices: 3206418--3206462 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3206408 GATCGTGGGT
*
3206418 TTTTTTTTTCATTTTTA
1 TTTTTTTTT-A-TTTGA
3206435 TTTTTTTTTATTTGA
1 TTTTTTTTTATTTGA
*
3206450 TTTTATTTTATTT
1 TTTTTTTTTATTT
3206463 CTAACCCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 16 0.62
16 1 0.04
17 9 0.35
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTATTTGA
Found at i:3217396 original size:12 final size:12
Alignment explanation
Indices: 3217379--3217429 Score: 75
Period size: 12 Copynumber: 4.2 Consensus size: 12
3217369 AATTTGATAA
*
3217379 TATTTATTTTAT
1 TATTTATTTAAT
*
3217391 TATTTATGTAAT
1 TATTTATTTAAT
3217403 TATTTATTTTAAT
1 TATTTA-TTTAAT
3217416 TATTTATTTAAT
1 TATTTATTTAAT
3217428 TA
1 TA
3217430 CAAAATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
12 24 0.69
13 11 0.31
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTTATTTAAT
Found at i:3217427 original size:25 final size:24
Alignment explanation
Indices: 3217379--3217429 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 24
3217369 AATTTGATAA
3217379 TATTTATTTTATTATTTATGTAAT
1 TATTTATTTTATTATTTATGTAAT
*
3217403 TATTTATTTTAATTATTTATTTAAT
1 TATTTATTTT-ATTATTTATGTAAT
3217428 TA
1 TA
3217430 CAAAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TATTTATTTTATTATTTATGTAAT
Found at i:3217465 original size:29 final size:28
Alignment explanation
Indices: 3217375--3217465 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 28
3217365 TTAAAATTTG
* *
3217375 ATAATATTTAT-TTTATTATTTA-TGTA
1 ATAATATTTTTATTTATTATTTATTATA
* * * *
3217401 ATTATTTATTTTAATTATTTATTTAATTACA
1 ATAATAT-TTTTATTTA-TTATTT-ATTATA
3217432 A-AATATTTTTATTTATTAGTTTATTATA
1 ATAATATTTTTATTTATTA-TTTATTATA
3217460 ATAATA
1 ATAATA
3217466 AATTTTCATT
Statistics
Matches: 48, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
26 5 0.10
27 3 0.06
28 12 0.25
29 21 0.44
30 4 0.08
31 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.59
Consensus pattern (28 bp):
ATAATATTTTTATTTATTATTTATTATA
Found at i:3217684 original size:11 final size:11
Alignment explanation
Indices: 3217668--3217701 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3217658 AAATATATAT
3217668 ATTTAAAATAA
1 ATTTAAAATAA
3217679 ATTT-AAATAA
1 ATTTAAAATAA
*
3217689 ATTTATAATAA
1 ATTTAAAATAA
3217700 AT
1 AT
3217702 ATTTTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTTAAAATAA
Found at i:3217688 original size:10 final size:10
Alignment explanation
Indices: 3217668--3217701 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
3217658 AAATATATAT
3217668 ATTTAAAATAA
1 ATTT-AAATAA
3217679 ATTTAAATAA
1 ATTTAAATAA
3217689 ATTTATAATAA
1 ATTTA-AATAA
3217700 AT
1 AT
3217702 ATTTTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 11 0.50
11 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:3218327 original size:22 final size:20
Alignment explanation
Indices: 3218299--3218343 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
3218289 AATATAATTT
3218299 AAAATTTTAATAAAAATTATAA
1 AAAATTTTAA-AAAAATTA-AA
*
3218321 AAAATTTTAACAAAATTAAA
1 AAAATTTTAAAAAAATTAAA
3218341 AAA
1 AAA
3218344 TATGTATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 7 0.32
22 10 0.45
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATTTTAAAAAAATTAAA
Done.